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Protocol describes sampling strategies, perservation and shipping of Acropora samples for Applied Biosystems™ Axiom™ Coral Genotyping Array – 550961 (384f) Applied Biosystems™ Axiom™ Coral Genotyping Array – 550962 (Mini 96) THIS PROTOCOL ACCOMPANIES THE FOLLOWING PUBLICATION Kitchen SA, Von Kuster G, Vasquez Kuntz KL, Reich HG, Miller W, Griffin S, Fogarty ND, Baums IB (2020) STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts. bioRxiv 10.1101/2020.01.21.914424:2020.2001.2021.914424. doi:10.1101/2020.01.21.914424. dx.doi.org/10.17504/protocols.io.bec8jazw 

DNA extraction protocol for Acropora tissue based on Qiagen DNAeasy kit THIS PROTOCOL ACCOMPANIES THE FOLLOWING PUBLICATION Baums IB, Hughes CR, Hellberg MH (2005) Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Mar Ecol Prog Ser 288:115-127. doi:10.3354/meps288115. dx.doi.org/10.17504/protocols.io.bcwuixew 

DNA extraction protocol for Acropora or other coral tissue based on Qiagen DNAeasy kit. This extraction protocol works well for the Acropora SNPchip and other coral genotyping applications (such as microsatellite genotyping). It preferrentially extracts coral host DNA but some Symbiodiniacea DNA will be present. THIS PROTOCOL ACCOMPANIES THE FOLLOWING PUBLICATION Baums IB, Hughes CR, Hellberg MH (2005) Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Mar Ecol Prog Ser 288:115-127. doi:10.3354/meps288115. dx.doi.org/10.17504/protocols.io.bgjqjumw 

Abstract Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral,Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two CaribbeanAcroporaspecies as well as their dominant dinoflagellate symbiont,Symbiodinium ‘fitti’.SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the generaBreviolum, Cladocopium, andDurusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called theStandardTools forAcroporidGenotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific. 

Abstract Foundation species such as redwoods, seagrasses and corals are often long‐lived and clonal. Genets may consist of hundreds of members (ramets) and originated hundreds to thousands of years ago. As climate change and other stressors exert selection pressure on species, the demography of populations changes. Yet, because size does not indicate age in clonal organisms, demographic models are missing data necessary to predict the resilience of many foundation species. Here, we correlate somatic mutations with genet age of corals and provide the first, preliminary estimates of genet age in a colonial animal. We observed somatic mutations at five microsatellite loci in rangewide samples of the endangered coral,Acropora palmata(n = 3352). Colonies harboured 342 unique mutations in 147 genets. Genet age ranged from 30 to 838 years assuming a mutation rate of 1.195⁻⁰⁴per locus per year based on colony growth rates and 236 to 6500 years assuming a mutation rate of 1.542⁻⁰⁵per locus per year based on sea level changes to habitat availability. Long‐livedA. palmatagenets imply a large capacity to tolerate past environmental change, and yet recent mass mortality events inA. palmatasuggest that capacity is now being frequently exceeded. 

Abstract Coral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross‐study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conservation strategies to mitigate coral bleaching worldwide.